Technical Abstract:
Phylogenies reconstructed with only one or a few independently inherited loci may be unresolved or incongruent due to data sampling, horizontal gene transfer, or differential selection and lineage sorting at individual loci. We examined the phylogenetic utility of conserved orthologous sequences (COS markers) in 37 diploid Solanum species in the sister clades tomato, potato, and outgroups. We analyzed 13 species of wild tomatoes (section Lycopersicon), four species in sections Juglandifolium and Lycopersicoides, 17 species of wild potatoes (section Petota), two species in section Etuberosum, and one species in the Dulcamara group; one species of Datura was used as outgroup. To date we have screened 88 COSII markers with a great variation in intron/exon content, varying in size from 600 to 1200 bp in length. We chose 48 of these by the presence of single band amplification as resolved in 1.5% agarose. We sequenced 23 of these 48 COSII that generated a total aligned length of 20,975 characters. Maximum-parsimony analyses of the concatenated dataset identified 2,630 parsimony informative characters, producing a tree of consistency index 0.83 and a retention index 0.86. Ingroup results are entirely in concordance with prior GBSSI sequence data for tomatoes and potatoes, except COS showed greatly increased resolution. Outgroup results were similar, but not entirely concordant with prior GBSSI and chloroplast DNA restriction site phylogenies. For example, COS placed sect. Lycopersicoides sister to tomatoes, in contrast to section Juglandifolium in GBSSI; but in both, sect. Etuberosum was sister to tomatoes and potatoes. We are performing additional phylogenetic analyses using Maximum Likelihood and Bayesian approaches, and assessing the congruence among COSII genes using the ILD and Bayesian Concordance Analysis.